The ionization potential of thymine functionalized at the C5 position with the truncated linker groups, -CH=CHCO2CH3 and -CH=CHCONHCH3, was examined using density functional theory. Results indicate that the addition of the carboxyl group to thymine lowers the adiabatic ionization potential by 0.4 eV. Further, modification of the carboxyl group by an amino group lowers the ionization potential by another 0.2 eV. The effect of solvation and base pairing with adenine on the modified thymine ionization energies was also investigated. The results provide evidence that linker groups can dampen the influence of adenine base pairing on thymine charge transfer. (C) 2003 Published by Elsevier B.V.